2.3. Bridging the gap: Molecular devices[[Student version, December 8, 2002]] 55
Figure 2.28:(Structure rendered from atomic coordinates.) Phosphoglycerate kinase. This enzyme performs one
of the steps in the glycolysis reaction; see Section 10.4. In this figure and Figure 2.29, hydrophobic carbon atoms are
white, mildly hydrophilic atoms are pastel (light blue for nitrogen and pink for oxygen), and strongly hydrophilic
atoms carrying a full electrical charge are brightly colored (blue for nitrogen and red for oxygen). The concept
of hydrophobicity, and the behavior of electrostatic charges in solution, are discussed in Chapter 7. Sulfur and
phosphate atoms are colored yellow. Hydrogen atoms are colored according to the atom to which they are bonded.
The enzyme manufactures one ATP molecule (green object) with each cycle of its action. [From (Goodsell, 1993)]
[Copyrighted figure; permission pending.]
Figure 2.29:(Composite of structures rendered from atomic coordinates.) A DNA-binding protein (10^7 ×magni-
fication). The color scheme is the same as Figure 2.28. Repressor proteins like this one bind directly to the DNA
double helix, physically blocking the polymerase that makes messenger RNA. They recognize a specific sequence of
DNA, generally blocking a region of 10–20 basepairs. The binding does not involve the formation of chemical bonds,
but rather uses the weaker interactions discussed in Chapter 7. Repressors form a molecular switch, turning off the
synthesis of a given protein until it is needed. [From (Goodsell, 1993).] [Copyrighted figure; permission pending.]